Mercurial > repos > bgruening > bismark
comparison bismark_methylation_extractor.py @ 22:8c191acde702 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35
| author | bgruening |
|---|---|
| date | Tue, 01 Aug 2023 11:42:10 +0000 |
| parents | 120b7b35e442 |
| children |
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| 21:120b7b35e442 | 22:8c191acde702 |
|---|---|
| 67 | 67 |
| 68 parser.add_argument("--multicore", dest="multicore", type=int, default=1) | 68 parser.add_argument("--multicore", dest="multicore", type=int, default=1) |
| 69 parser.add_argument("--splitting_report", dest="splitting_report") | 69 parser.add_argument("--splitting_report", dest="splitting_report") |
| 70 parser.add_argument("--mbias_report", dest="mbias_report") | 70 parser.add_argument("--mbias_report", dest="mbias_report") |
| 71 parser.add_argument("--cytosine_report", dest="cytosine_report") | 71 parser.add_argument("--cytosine_report", dest="cytosine_report") |
| 72 parser.add_argument("--coverage_file", dest="coverage_file") | |
| 73 | |
| 72 parser.add_argument("--genome_file", dest="genome_file") | 74 parser.add_argument("--genome_file", dest="genome_file") |
| 73 parser.add_argument("--cx_context", action="store_true") | 75 parser.add_argument("--cx_context", action="store_true") |
| 74 | 76 |
| 75 parser.add_argument("--comprehensive", action="store_true") | 77 parser.add_argument("--comprehensive", action="store_true") |
| 76 parser.add_argument("--merge-non-cpg", dest="merge_non_cpg", action="store_true") | 78 parser.add_argument("--merge-non-cpg", dest="merge_non_cpg", action="store_true") |
| 131 cmd.extend( | 133 cmd.extend( |
| 132 [ | 134 [ |
| 133 "--bedGraph", | 135 "--bedGraph", |
| 134 "--CX_context", | 136 "--CX_context", |
| 135 "--cytosine_report", | 137 "--cytosine_report", |
| 136 "--CX_context", | |
| 137 "--genome_folder", | 138 "--genome_folder", |
| 138 tmp_genome_dir, | 139 tmp_genome_dir, |
| 139 ] | 140 ] |
| 140 ) | 141 ) |
| 141 else: | 142 else: |
| 173 if args.cx_context: | 174 if args.cx_context: |
| 174 shutil.move( | 175 shutil.move( |
| 175 glob(os.path.join(output_dir, "*CX_report.txt"))[0], | 176 glob(os.path.join(output_dir, "*CX_report.txt"))[0], |
| 176 args.cytosine_report, | 177 args.cytosine_report, |
| 177 ) | 178 ) |
| 179 | |
| 178 else: | 180 else: |
| 179 shutil.move( | 181 shutil.move( |
| 180 glob(os.path.join(output_dir, "*CpG_report.txt"))[0], | 182 glob(os.path.join(output_dir, "*CpG_report.txt"))[0], |
| 181 args.cytosine_report, | 183 args.cytosine_report, |
| 182 ) | 184 ) |
| 185 | |
| 186 # coverage file | |
| 187 if args.coverage_file: | |
| 188 shutil.move( | |
| 189 glob(os.path.join(output_dir, "*datbismark.cov.gz"))[0], | |
| 190 args.coverage_file, | |
| 191 ) | |
| 192 | |
| 183 # splitting report | 193 # splitting report |
| 184 if args.splitting_report: | 194 if args.splitting_report: |
| 185 logger.debug("Collecting splitting report.") | 195 logger.debug("Collecting splitting report.") |
| 186 shutil.move( | 196 shutil.move( |
| 187 glob(os.path.join(output_dir, "*_splitting_report.txt"))[0], | 197 glob(os.path.join(output_dir, "*_splitting_report.txt"))[0], |